Python库 | aiida-optimade-0.15.0.tar.gz

# OPTIMADE API implementation for AiiDA | Latest release | Build status | Activity | |:--------------:|:------------:|:--------:| | [](https://github.com/aiidateam/aiida-core/)<br>[](https://pypi.org/project/aiida-optimade/)<br>[](https://pypi.org/project/aiida-optimade/)<br>[](https://github.com/Materials-Consortia/OPTIMADE/) | [](https://github.com/aiidateam/aiida-optimade/actions/)<br>[](https://codecov.io/gh/aiidateam/aiida-optimade) | [](https://github.com/aiidateam/aiida-optimade) | This is a RESTful API server created with [FastAPI](https://fastapi.tiangolo.com/) that exposes an AiiDA database according to the [OPTIMADE specification](https://github.com/Materials-Consortia/OPTIMADE/blob/develop/optimade.rst). It is mainly used by [Materials Cloud](https://www.materialscloud.org/) to expose access to archived AiiDA databases through the OPTIMADE API. But it may be freely implemented by any to fulfill a similar purpose. The server is based on the test server "template" used in the [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools) package. Indeed, the filter grammar and parser and [`pydantic`](https://pydantic-docs.helpmanual.io/) models from [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools) are used directly here. ## Prerequisites Environment where AiiDA is installed. AiiDA database containing `StructureData` nodes, since these are the _only_ AiiDA nodes that are currently exposed with this API (under the `/structures` endpoint). ## Installation The package is relased on PyPI, hence you can install it by: ```shell $ pip install aiida-optimade ``` Otherwise, you can also `git clone` the repository from GitHub: ```shell $ git clone https://github.com/aiidateam/aiida-optimade /path/to/aiida-optimade/parent/dir $ pip install -e /path/to/aiida-optimade ``` ### Development For developers, there is a special setuptools extra `dev`, which can be installed by: ```shell $ pip install aiida-optimade[dev] ``` or ```shell $ pip install -e /path/to/aiida-optimade[dev] ``` This package uses [Black](https://black.readthedocs.io/en/stable/) for formatting. If you wish to contribute, please install the git pre-commit hook: ```shell /path/to/aiida-optimade$ pre-commit install ``` This will automatically update the formatting when running `git commit`, as well as check the validity of various repository JSON and YAML files. ## Initialization You should first initialize your AiiDA profile. This can be done by using the `aiida-optimade` CLI: ```shell $ aiida-optimade -p <PROFILE> init ``` Where `<PROFILE>` is the AiiDA profile. > **Note**: Currently, the default is `optimade_sqla`, if the `-p / --profile` option is now specified. > This will be changed in the future to use the default AiiDA profile. Initialization goes through your profile's `StructureData` nodes, adding an `optimade` extra, wherein all OPTIMADE-specific fields that do not have an equivalent AiiDA property are stored. If in the future, more `StructureData` nodes are added to your profile's database, these will be automatically updated for the first query, filtering on any of these OPTIMADE-specific fields. However, if you do not wish a significant lag for the user or risking several GET requests coming in at the same time, trying to update your profile's database, you should re-run `aiida-optimade init` for your profile (in between shutting the server down and restarting it again). ## Running the server ### Locally Using the `aiida-optimade` CLI, you can do the following: ```shell $ aiida-optimade -p <PROFILE> run ``` Where `<PROFILE>` is the AiiDA profile you wish to serve. > **Note**: Currently, the default is `optimade_sqla`, if the `-p / --profile` option is now specified. > This will be changed in the future to use the default AiiDA profile. You also have the opportunity to specify the AiiDA profile via the environment variable `AIIDA_PROFILE`. Note, however, that if a profile name is passed to the CLI, it will overrule _and replace_ the current `AIIDA_PROFILE` environment variable. ```shell # Specifying AiiDA profile as an environment variable $ export AIIDA_PROFILE=optimade $ aiida-optimade run ``` Navigate to `http://localhost:5000/v1/info` > **Tip**: To see the default AiiDA profile, type `verdi profile list` to find the colored profile name marked with an asterisk (`*`), or type `verdi profile show`, which will show you more detailed information about the default profile. > **Note**: The `aiida-optimade run` command has more options to configure your server, run > > ```shell > $ aiida-optimade run --help > ``` > > for more information. ### With Docker Adapt `profiles/test_django.json` and `profiles/docker-compose.yml` appropriately. ```shell $ docker-compose -f profiles/docker-compose.yml up --build ``` Navigate to `http://localhost:3253/v1/info` Stop by using ```shell $ docker-compose -f profiles/docker-compose.yml down ``` #### Jinja templates If you are familiar with [Jinja](https://palletsprojects.com/p/jinja/), there are two templates to create the JSON and YAML files: `profiles/config.j2` and `profiles/docker-compose.j2`, respectively. ## Configure the server You can configure the server with the `aiida_optimade/config.json` file or set certain environment variables. To learn more about this, see the [`optimade-python-tools`](https://github.com/Materials-Consortia/optimade-python-tools) repository. ## Design choices **Q: Why create an individual `config.json` file instead of just mounting an existing `.aiida` directory and using that directly?** **A:** This, currently, wouldn't work because the `REPOSITORY_URI` needs to point to the right path *inside* the container, not on the host. Furthermore, storing all configurations in the same file can be fragile.